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diff --git a/python-pdb-profiling.spec b/python-pdb-profiling.spec new file mode 100644 index 0000000..7c234f1 --- /dev/null +++ b/python-pdb-profiling.spec @@ -0,0 +1,414 @@ +%global _empty_manifest_terminate_build 0 +Name: python-pdb-profiling +Version: 0.4.4 +Release: 1 +Summary: Profiling Protein Structures from Protein Data Bank and integrate various resources.🏄♂️ +License: MIT +URL: https://github.com/NatureGeorge/pdb-profiling +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/e1/47/613f1ea5cb7b8bd7dc4dd2af58f678ec82234fb2df62755d22e3958cfa29/pdb_profiling-0.4.4.tar.gz +BuildArch: noarch + + +%description +# pdb-profiling + +[](https://zenodo.org/badge/latestdoi/247475852) +[](https://github.com/naturegeorge/pdb-profiling/blob/master/LICENSE) +[](https://pypi.org/project/pdb-profiling/) +[](https://github.com/naturegeorge/pdb-profiling/blob/master/pdb_profiling/__init__.py) +[](https://pypi.org/project/pdb-profiling/) +[](https://github.com/NatureGeorge/pdb-profiling/releases/) +[](https://github.com/naturegeorge/pdb-profiling) +[](https://coveralls.io/github/NatureGeorge/pdb-profiling?branch=master) + + + +Profiling Protein Structures from Protein Data Bank and integrate various resources. + +## Features + +* `Collection`: Implement various API to collect the well-organized metadata of PDB in real time. +* `Integration`: Provide a unified call for API-interface and return-data-form as well as subsequent data processing. +* `Detection`: Reorganize metadata to evaluate a PDB structure in Entry-Assembly/Model-Entity-Chain-Residue level and integrated with UniProt-KB. +* `Interaction`: Include UniProt Isoform Interaction in Asymmetric unit plus Biological Assembly level. +* `Selection`: Define the representative set of PDB structures in Monomeric|Homomeric|Heteromeric states. +* `Mapping`: Provide interface for both entry-identifier/accession-level and residue-level bidirectional mapping. + +## Install + +> Notice: require Python Environment >= 3.7, Platform Independent + +Install by `pip` command. + +### *Before your Installation + +* Make sure that your 64-bit machine is installed with 64-bit Python. +* To avoid some unexpected issues, you should upgrade your `pip` beforehand: + +```bash +python -m pip install --upgrade pip +``` + +### Official Installation + +```bash +python -m pip install pdb-profiling +``` + +If you have already installed an older version of `pdb-profiling`, use the following command to install the latest version: + +```bash +python -m pip install --upgrade pdb-profiling +``` + +### Build From Source (optional, for non-windows environment) + +```bash +python -m pip install cython +python -m pip install numpy +git clone https://github.com/NatureGeorge/pdb-profiling.git +python setup.py build_ext --inplace # Need GCC or Other Compiler For C +python setup.py install # or "sudo python setup.py install" or "python setup.py install --user" +``` + +## Documentation + +<https://pdb-profiling.netlify.app/> + +## Examples + +### Basic Usage + +* [Command Line Example](https://github.com/NatureGeorge/pdb-profiling/discussions/2) +* [Retrieve Bound Molecule Data From PDBe](https://github.com/NatureGeorge/pdb-profiling/discussions/3) +* ... + +### Large-Scale-Example + +* [ExAC](https://github.com/NatureGeorge/pdb-profiling/blob/master/examples/exac_example.md) + +## Resources + +* PDBe Entry-Based API +* PDBe Aggregated API (PDBe Graph API) +* PDBe ModelServer API +* SWISS-MODEL Repository API +* UniProt API +* EBI Proteins API +* RCSB Data API +* RCSB Search API +* Eutils API (minimum usage) +* ... + +> click [here](https://pdb-profiling.netlify.app/docs/5-reference/) for more details + +## Related Resources + +> Using similar data resources but meant to achieve different goals. + +<details> + +<summary>Click to view</summary> + +* `RCSB`: [Build Customize Tabular Reports of PDB Data](https://www.rcsb.org/news?year=2020&article=5f6529e207302466657ec0e9&feature=true) +* [MolArt](https://github.com/davidhoksza/MolArt) + +</details> + +## Copyright Notice + +This project is developed by [Zefeng Zhu](https://github.com/NatureGeorge) and hold by [Minghui Group](https://lilab.jysw.suda.edu.cn/). + +## License + +The `pdb_profiling.cython.py_qcprot` module is derived from the [cython wrapper contributed by Bernhard Thiel](https://github.com/Bernhard10/py_qcprot) and is distributed under the terms of a BSD-3-Clause License. And it also contains the dependent C-code from <http://theobald.brandeis.edu/QCP/> written by Pu Liu and Douglas Theobald (with slight modification by Bernhard Thiel) and is licensed under a BSD-3-Clause License. + +The `pdb_profiling` is distributed under the terms of the MIT License. + + +%package -n python3-pdb-profiling +Summary: Profiling Protein Structures from Protein Data Bank and integrate various resources.🏄♂️ +Provides: python-pdb-profiling +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-pdb-profiling +# pdb-profiling + +[](https://zenodo.org/badge/latestdoi/247475852) +[](https://github.com/naturegeorge/pdb-profiling/blob/master/LICENSE) +[](https://pypi.org/project/pdb-profiling/) +[](https://github.com/naturegeorge/pdb-profiling/blob/master/pdb_profiling/__init__.py) +[](https://pypi.org/project/pdb-profiling/) +[](https://github.com/NatureGeorge/pdb-profiling/releases/) +[](https://github.com/naturegeorge/pdb-profiling) +[](https://coveralls.io/github/NatureGeorge/pdb-profiling?branch=master) + + + +Profiling Protein Structures from Protein Data Bank and integrate various resources. + +## Features + +* `Collection`: Implement various API to collect the well-organized metadata of PDB in real time. +* `Integration`: Provide a unified call for API-interface and return-data-form as well as subsequent data processing. +* `Detection`: Reorganize metadata to evaluate a PDB structure in Entry-Assembly/Model-Entity-Chain-Residue level and integrated with UniProt-KB. +* `Interaction`: Include UniProt Isoform Interaction in Asymmetric unit plus Biological Assembly level. +* `Selection`: Define the representative set of PDB structures in Monomeric|Homomeric|Heteromeric states. +* `Mapping`: Provide interface for both entry-identifier/accession-level and residue-level bidirectional mapping. + +## Install + +> Notice: require Python Environment >= 3.7, Platform Independent + +Install by `pip` command. + +### *Before your Installation + +* Make sure that your 64-bit machine is installed with 64-bit Python. +* To avoid some unexpected issues, you should upgrade your `pip` beforehand: + +```bash +python -m pip install --upgrade pip +``` + +### Official Installation + +```bash +python -m pip install pdb-profiling +``` + +If you have already installed an older version of `pdb-profiling`, use the following command to install the latest version: + +```bash +python -m pip install --upgrade pdb-profiling +``` + +### Build From Source (optional, for non-windows environment) + +```bash +python -m pip install cython +python -m pip install numpy +git clone https://github.com/NatureGeorge/pdb-profiling.git +python setup.py build_ext --inplace # Need GCC or Other Compiler For C +python setup.py install # or "sudo python setup.py install" or "python setup.py install --user" +``` + +## Documentation + +<https://pdb-profiling.netlify.app/> + +## Examples + +### Basic Usage + +* [Command Line Example](https://github.com/NatureGeorge/pdb-profiling/discussions/2) +* [Retrieve Bound Molecule Data From PDBe](https://github.com/NatureGeorge/pdb-profiling/discussions/3) +* ... + +### Large-Scale-Example + +* [ExAC](https://github.com/NatureGeorge/pdb-profiling/blob/master/examples/exac_example.md) + +## Resources + +* PDBe Entry-Based API +* PDBe Aggregated API (PDBe Graph API) +* PDBe ModelServer API +* SWISS-MODEL Repository API +* UniProt API +* EBI Proteins API +* RCSB Data API +* RCSB Search API +* Eutils API (minimum usage) +* ... + +> click [here](https://pdb-profiling.netlify.app/docs/5-reference/) for more details + +## Related Resources + +> Using similar data resources but meant to achieve different goals. + +<details> + +<summary>Click to view</summary> + +* `RCSB`: [Build Customize Tabular Reports of PDB Data](https://www.rcsb.org/news?year=2020&article=5f6529e207302466657ec0e9&feature=true) +* [MolArt](https://github.com/davidhoksza/MolArt) + +</details> + +## Copyright Notice + +This project is developed by [Zefeng Zhu](https://github.com/NatureGeorge) and hold by [Minghui Group](https://lilab.jysw.suda.edu.cn/). + +## License + +The `pdb_profiling.cython.py_qcprot` module is derived from the [cython wrapper contributed by Bernhard Thiel](https://github.com/Bernhard10/py_qcprot) and is distributed under the terms of a BSD-3-Clause License. And it also contains the dependent C-code from <http://theobald.brandeis.edu/QCP/> written by Pu Liu and Douglas Theobald (with slight modification by Bernhard Thiel) and is licensed under a BSD-3-Clause License. + +The `pdb_profiling` is distributed under the terms of the MIT License. + + +%package help +Summary: Development documents and examples for pdb-profiling +Provides: python3-pdb-profiling-doc +%description help +# pdb-profiling + +[](https://zenodo.org/badge/latestdoi/247475852) +[](https://github.com/naturegeorge/pdb-profiling/blob/master/LICENSE) +[](https://pypi.org/project/pdb-profiling/) +[](https://github.com/naturegeorge/pdb-profiling/blob/master/pdb_profiling/__init__.py) +[](https://pypi.org/project/pdb-profiling/) +[](https://github.com/NatureGeorge/pdb-profiling/releases/) +[](https://github.com/naturegeorge/pdb-profiling) +[](https://coveralls.io/github/NatureGeorge/pdb-profiling?branch=master) + + + +Profiling Protein Structures from Protein Data Bank and integrate various resources. + +## Features + +* `Collection`: Implement various API to collect the well-organized metadata of PDB in real time. +* `Integration`: Provide a unified call for API-interface and return-data-form as well as subsequent data processing. +* `Detection`: Reorganize metadata to evaluate a PDB structure in Entry-Assembly/Model-Entity-Chain-Residue level and integrated with UniProt-KB. +* `Interaction`: Include UniProt Isoform Interaction in Asymmetric unit plus Biological Assembly level. +* `Selection`: Define the representative set of PDB structures in Monomeric|Homomeric|Heteromeric states. +* `Mapping`: Provide interface for both entry-identifier/accession-level and residue-level bidirectional mapping. + +## Install + +> Notice: require Python Environment >= 3.7, Platform Independent + +Install by `pip` command. + +### *Before your Installation + +* Make sure that your 64-bit machine is installed with 64-bit Python. +* To avoid some unexpected issues, you should upgrade your `pip` beforehand: + +```bash +python -m pip install --upgrade pip +``` + +### Official Installation + +```bash +python -m pip install pdb-profiling +``` + +If you have already installed an older version of `pdb-profiling`, use the following command to install the latest version: + +```bash +python -m pip install --upgrade pdb-profiling +``` + +### Build From Source (optional, for non-windows environment) + +```bash +python -m pip install cython +python -m pip install numpy +git clone https://github.com/NatureGeorge/pdb-profiling.git +python setup.py build_ext --inplace # Need GCC or Other Compiler For C +python setup.py install # or "sudo python setup.py install" or "python setup.py install --user" +``` + +## Documentation + +<https://pdb-profiling.netlify.app/> + +## Examples + +### Basic Usage + +* [Command Line Example](https://github.com/NatureGeorge/pdb-profiling/discussions/2) +* [Retrieve Bound Molecule Data From PDBe](https://github.com/NatureGeorge/pdb-profiling/discussions/3) +* ... + +### Large-Scale-Example + +* [ExAC](https://github.com/NatureGeorge/pdb-profiling/blob/master/examples/exac_example.md) + +## Resources + +* PDBe Entry-Based API +* PDBe Aggregated API (PDBe Graph API) +* PDBe ModelServer API +* SWISS-MODEL Repository API +* UniProt API +* EBI Proteins API +* RCSB Data API +* RCSB Search API +* Eutils API (minimum usage) +* ... + +> click [here](https://pdb-profiling.netlify.app/docs/5-reference/) for more details + +## Related Resources + +> Using similar data resources but meant to achieve different goals. + +<details> + +<summary>Click to view</summary> + +* `RCSB`: [Build Customize Tabular Reports of PDB Data](https://www.rcsb.org/news?year=2020&article=5f6529e207302466657ec0e9&feature=true) +* [MolArt](https://github.com/davidhoksza/MolArt) + +</details> + +## Copyright Notice + +This project is developed by [Zefeng Zhu](https://github.com/NatureGeorge) and hold by [Minghui Group](https://lilab.jysw.suda.edu.cn/). + +## License + +The `pdb_profiling.cython.py_qcprot` module is derived from the [cython wrapper contributed by Bernhard Thiel](https://github.com/Bernhard10/py_qcprot) and is distributed under the terms of a BSD-3-Clause License. And it also contains the dependent C-code from <http://theobald.brandeis.edu/QCP/> written by Pu Liu and Douglas Theobald (with slight modification by Bernhard Thiel) and is licensed under a BSD-3-Clause License. + +The `pdb_profiling` is distributed under the terms of the MIT License. + + +%prep +%autosetup -n pdb-profiling-0.4.4 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-pdb-profiling -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Fri May 05 2023 Python_Bot <Python_Bot@openeuler.org> - 0.4.4-1 +- Package Spec generated |